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Topic: Sequence motif

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Sequence analysis

Sequence database

Sequence alignment

Repeated Sequences

Blast

Genetic code

Gene regulatory network

Sequencing

Hidden Markov model

Bayesian network

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	Sequence motif
		A sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.
		When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
		Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation.
	www.ibpassociation.org /encyclopedia/Biotechnology/Sequence_motif.php (991 words)

	MotifViz
		Which background sets to use depends on which sequences you are studying: they should ideally come from the same taxonomic group as the target sequences, and have similar repetitive element and GC content.
		Clover requires background sequences to be much longer than query sequences (at least one sequence in each background set must be longer than the longest query sequence), and it processes each background set separatedly.
		When shuffling a motif, the counts of A, C, G and T within each position are not shuffled, but the positions are shuffled among one another.
	biowulf.bu.edu /MotifViz (1507 words)

	Sequence motif - Wikipedia, the free encyclopedia
		In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.
		A motif discovery algorithm that considers phylogenetic conservation is PhyloGibbs.
		A cutoff is needed to specify whether an input sequence matches the motif or not.
	en.wikipedia.org /wiki/Sequence_motif (1208 words)

	BioMed Central \| Full text \| CoSMoS: Conserved Sequence Motif Search in the proteome
		But if a sequence motif is highly conserved over a wide stretch of evolutionary distant proteins, it is likely that it plays an important role as part of an active site, a site of regulation or a substrate and cofactor binding site.
		The calculations of the multiple sequence alignments were performed on 6 nodes of the nyx opteron cluster at the Center for Advanced Computing at the University of Michigan.
		Then the whole proteome is searched for that specific motif and all the instances are displayed ordered by their evolutionary significance to make it easy for the user to distinguish between proteins with a purely statistical and proteins with a functionally relevant occurrence of this motif.
	www.biomedcentral.com /1471-2105/7/37 (2818 words)

	Current Protocols in Bioinformatics: MEME
		A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group.
		MEME looks for the most "significant" motifs in the input sequences, where "significant" is a function of the length of the pattern, number of times it occurs and degree of similarity among the occurrences.
		For a motif to be useful for database searches, it must as a rule contain at least log_2(N) bits of information where N is the number of sequences in the database being searched.
	www.sdsc.edu /~tbailey/MEME-protocol-draft2/protocols.html (6639 words)

	Sequence alignment - Wikipedia, the free encyclopedia
		In bioinformatics, a sequence alignment is a way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
		If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another.
		In protein sequence alignment, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages.
	en.wikipedia.org /wiki/Sequence_alignment (4439 words)

	Use of motifs in sequence analysis (Site not responding. Last check: 2007-10-05)
		Historically, computational motif analysis was used for the detection of related sequences, whose similarity to the query sequences was too low as to be detected with the classical methods like BLAST or FASTA.
		Motif analysis relies on the identification of small conserved regions in the proteins that can be identified in remote homologous, despite the lack of overall similarity.
		At the same time, the motifs exist because of particular requirements on the structure of specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity.
	www.pdg.cnb.uam.es /cursos/Generic2000/SeqAlign.html (3298 words)

	A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes -- Hajarnavis and Durbin ...
		A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes -- Hajarnavis and Durbin 12 (10): 1786 -- RNA
		tract from 625 mRNA sequences of non-Caenorhabditis ribosomal
		The UUGUU motif is reminiscent in its composition of the GU-rich
	www.rnajournal.org /cgi/content/full/12/10/1786 (1688 words)

	MEME
		If your sequence(s) are not the correct type, turn to Appendix VI for information on how to change or set the type of a sequence.
		MEME can either a) favor motifs that appear exactly once in each sequence in the training set (the one-per model); b) favor motifs that appear zero or one time in each sequences in the training set (the zero-or-one-per model); or c) give no preference to the number of occurrences (the zero-or-more-per model).
		If a given motif scores well at more than one position in a sequence, the motif might still be chosen, but the additional scores "hits" will not contribute to its score.
	rcr-www.med.nyu.edu /rcr/gcg/meme.html (3114 words)

	InterPro: IPR006594 Lissencephaly type-1-like homology motif (Site not responding. Last check: 2007-10-05)
		It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerization, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
		The predicted secondary structure of LisH motifs, and their occurrence in homologues of Gbeta beta-propeller subunits, suggests that they are analogues of Ggamma subunits, and might associate with the periphery of beta-propeller domains.
		The average number of amino acids overlapping in the sequences of the 31 proteins common to both entries is then calculated, with the results displayed in the bar diagram on the right.
	www.ebi.ac.uk /interpro/IEntry?ac=IPR006594 (3071 words)

	Association of a Model Transmembrane Peptide Containing Gly in a Heptad Sequence Motif Biophysical Journal - Find ...
		A peptide containing glycine at a and d positions of a heptad motif was synthesized to investigate the possibility that membrane-soluble peptides with a Gly-based, left-handed helical packing motif would associate.
		Applying this treatment to the FRET data, constraining the dimerization constant to be within experimental uncertainty of that measured by analytical ultracentrifugation, we found the data could be well described by a monomer-dimer equilibrium with only partial quenching of the dimer, suggesting that the helices are most probably antiparallel.
		More generally, the motif GxxxG appears to be a common theme in the association of helical membrane proteins (Brosig and Langosch, 1998; Javadpour et al., 1999; Langosch et al., 1996; Russ and Engelman, 2000; Senes et al., 2000).
	www.findarticles.com /p/articles/mi_qa3938/is_200411/ai_n9463153 (910 words)

	A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear ...
		A sequence motif conserved in diverse nuclear proteins identifies a protein interaction domain utilised for nuclear targeting by human TFIIS -- Ling et al.
		The extent of the LW motif is indicated by arrows above a CLUSTALW 1.7 (47) alignment that was manually adjusted to position any gaps to the interhelical linker regions of the structure predicted for this region of human TFIIS (17).
		The region containing the highly conserved sequence present in both yeast and human and that includes the LW motif is shaded, and two other well-conserved regions that flank an extensive region possessing many acidic residues are indicated by hatching.
	nar.oxfordjournals.org /cgi/content/full/34/8/2219 (6208 words)

	A Sequence Motif within Trypanosome Precursor tRNAs Influences Abundance and Mitochondrial Localization -- Sherrer et ...
		by sequences or nucleotide modifications that inhibit import (12).
		The resulting sequences were analyzed with tRNAScan-SE to predict the presence of tRNA genes (17).
		Mutation of the YGG(C/A)RRC motif in the 5' flanking sequence of tRNA
	mcb.asm.org /cgi/content/full/23/24/9061 (6338 words)

	A general procedure for locating and analyzing protein-binding sequence motifs in nucleic acids -- O'Neill 95 (18): ...
		Gatlin (1) first recognized that the Shannon expression for string entropy might prove useful in sequence analysis.
		Suppose we consider a simple example, a motif 3 bases long with five known members of the family.
		be seen by using the entire sequences as opposed to disjoint half-sequences.
	www.pnas.org /cgi/content/full/95/18/10710 (4866 words)

	Construction of a sequence motif characteristic of aminergic G protein-coupled receptors -- Huang 12 (7): 1360 -- ...
		Construction of a sequence motif characteristic of aminergic G protein-coupled receptors -- Huang 12 (7): 1360 -- Protein Science
		Construction of a sequence motif characteristic of aminergic G protein–coupled receptors
		Kuipers, W., Oliveira, L., Vriend, G., and Ijzerman, A.P. Identification of class-determining residues in G protein–coupled receptors by sequence analysis.
	www.proteinscience.org /cgi/content/full/12/7/1360 (3426 words)

	EMBOSS: patmatmotifs
		These motifs arise because of particular requirements on the structure of specific region(s) of a protein which may be important, for example, for their binding properties or for their enzymatic activity.
		The use of protein sequence patterns (or motifs) to determine the function(s) of proteins is becoming very rapidly one of the essential tools of sequence analysis.
		It is common to find that a search of the PROSITE database against a protein sequence will report many matches to the short motifs that are indicative of the post-translational modification sites, such as glycolsylation, myristylation and phosphorylation sites.
	www.psc.edu /general/software/packages/emboss/patmatmotifs.html (929 words)

	PRINTS
		A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite.
		Usually the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space.
		Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours.
	www.bioinf.manchester.ac.uk /dbbrowser/PRINTS (108 words)

	MOTIF: Searching Protein and Nucleic Acid Sequence Motifs (Site not responding. Last check: 2007-10-05)
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	motif.genome.ad.jp (67 words)

	DNA Sequence & Structural Analyses
		DNA Sequence Translation - Analysis of ORF in Gene Sequence - U Minnesota (US)
		Prediction of Gene Structure in DNA Sequence from
		Prediction of Potential 5'-,Internal, & 3'-Exons in DNA sequence from
	restools.sdsc.edu /biotools/biotools16.html (969 words)

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